Table 1.
Sample descriptives and genotyping procedures in four studies of alcohol use disorders.
| ALSPAC | FT12 | COGA | IASPSAD | |
|---|---|---|---|---|
| N | 4,304 | 1,135 | 2,097 | 706 |
| % Female | 57.0 | 53.6 | 53.6 | 34.3 |
| Mean age (SD) | 17.9 | 22.4 | 35.1 | 41.8 |
| Recruitment strategy | Birth cohort | Twin birth cohort | Families of treatment-seeking patients | Siblings of treatment-seeking patients |
| Phenotype | Factor score of DSM-IV and AUDIT AD symptoms | DSM-IV AD symptoms | DSM-IV AD symptoms | DSM-IV AD symptoms |
| Genotyping platform | Illumina Human Hap550 Quada | Illumina Human670-QuadCustom BeadChipa | Illumina Human OmniExpress array 12.VIa; Illumina Human 1M-Duo BeadChipa | Affymetrix Human SNP Array 6.0b |
| Quality control filtering | MAF < 1%, call rate < 95%, HWE p < 5 × 10−7, missingness > 3%, heterozygosity outliers, gender mismatch, cryptic relatedness (IBD > 10%) | MAF < 1%, call rate < 95%, HWE p < 10−6, missingness > 5%, heterozygosity outliers, gender mismatch, cryptic relatedness (outside of known families) | MAF < 5%, GenCall score < .15, HWE p < 10−6, inconsistent calls between Omni and 1M arrays, Mendelian errors, cryptic relatedness (outside of known families) | MAF < 1%, call rate < 97%, HWE p < 10−6, missingness > 3%, cryptic relatedness (IBD > 5% outside of known families) |
| 1000 Genomes version | Phase 1 v3, March 2012 | Phase 1 v3, March 2012 | Phase 1 v2, December 2010 (EUR) | Phase 1 v3, March 2012 |
| Reference genome build | GRCh37 | GRCh37 | GRCh37 | GRCh37 |
| Imputation software | MACH/Minimacc | ShapeITe; IMPUTE2f | BEAGLE 3.3.1d | ShapeITe; IMPUTE2f |
| Number of imputed SNPs | 8,458,542 (MAF>.01) | 6,729,635 (MAF>.01) | 4,150,783 (MAF>.05) | 8,347,617 (MAF>.01) |
| Reference for full genotyping details | Edwards et al. (2015); Fatemifar et al. (2013) | Salvatore et al. (2014); Konttinen et al. (2015) | Kapoor et al. (2014); Wang et al. (2013) | Adkins et al. (2017) |
AD = alcohol dependence, MAF = minor allele frequency, HWE = Hardy-Weinberg equilibrium, IBD = identity-by-descent, SNP = single nucleotide polymorphism.
a
Illumina, Inc., San Diego, CA, USA,
b
Affymetrix, Santa Clara, CA, USA,
d
Browning & Browning, 2007,
e
Delaneau et al., 2012,
f
Howie et al., 2009